6-87477166-G-GGTGT

Variant names:

• chr6-87477166-G-GGTGT
• rs71018020
• NM_006416.5:c.17-174_17-171dupTGTG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006416.5(SLC35A1):​c.17-174_17-171dupTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.37 (10103 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0780

Genes affected

SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]

ENSG00000213204 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-87477166-G-GGTGT is Benign according to our data. Variant chr6-87477166-G-GGTGT is described in ClinVar as [Benign]. Clinvar id is 1174350.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-174_17-171dupTGTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-174_17-171dupTGTG		intron_variant	Intron 1 of 6		NP_001161870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A1	ENST00000369552.9	c.17-196_17-195insGTGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-196_*61-195insGTGT		intron_variant	Intron 13 of 15	2		ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55210 AN: 149604 Hom.: 10096 Cov.: 0

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.388

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 55228 AN: 149708 Hom.: 10103 Cov.: 0 AF XY: 0.370 AC XY: 26961 AN XY: 72938

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.390

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 23, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71018020; hg19: chr6-88186884;